Team Dark: Agents of GUN
by TheRedeemer1995
Summary: After the events of the Black Arms Invasion, Shadow was recruited into the service of the Guardian Units of Nations as part of their elite strike team, codenamed "Team Dark," alongside Rouge the Bat and E-123 Omega. The team swiftly rose through the ranks and became one of GUN's most effective and ruthless units. But, now, Team Dark will face their ultimate test: The Dark Legion.
1. Prologue: Enlisted

_**Greetings, prospective readers, and welcome to my very first Sonic the Hedgehog project. Admittedly, this one has been one that I've been toying with for quite some time, and now, at last, it is ready to be unleashed! Well, to time to sit about babbling, let us begin!**_

 _Prologue: Enlisted_

On a forest road somewhere, a motorcycle raced past countless trees, cars, and other vehicles. Riding the motorcycle was a what looked to be an jet-black anthropomorphic hedgehog with crimson highlights in his quills. He wore a pair of black leather gloves, red and white Hover Shoes, black pants with a black leather belt, a white shirt, and a black and red leather overcoat. His name was Shadow the Hedgehog and he was the Ultimate Life Form, originally created to cure a rare disease known as NIDS, but later converted into a secret military weapons project designed to create the ultimate supersoldier… before the project was terminated, along with everyone involved in it. Among those who were killed was someone Shadow once felt close to: a girl named Maria Robotnik, the granddaughter of his creator, Gerald Robotnik, who had been shot right in front of Shadow, the memory of which was the only truly clear one in Shadow's mind.

Shadow continued his journey to who-knew-where, thinking back to the events of two weeks ago. He had only stopped in Westopolis for a drink and to maybe see what this whole "Fire In The Sky" festival, which apparently revolved around a special black comet that only passed Mobius every half century, was all about.

But, he ended up getting more than he bargained for when the sky opened up and thousands of black and red aliens started dropping down from it. At the time he didn't see how they could concern him but then… _he_ showed up. The leader of the Black Arms, Black Doom. His… father.

Black Doom had wanted Shadow to find the seven Chaos Emeralds and deliver them to him. Shadow smirked as he thought of this detail. Was there _ever_ going to be a global threat that didn't involve the Chaos Emeralds in some way, shape, or form? Meanwhile, Sonic and his gang were fighting off the Black Arms alongside the Guardian Units of Nations, or GUN for short. Unfortunately, they hadn't done a very good job. GUN's mainframe had been sabotaged, and many innocents had been killed by the Black Arms, especially in Westopolis, where the defense system had been knocked out.

Despite his want to keep out of things such as this, he tagged along because of one thing. Black Doom promised to tell Shadow his past, and to help him regain the memories that he'd lost after he fell from the Space Colony ARK. But, what he discovered haunts him to this very day. As it was revealed to him, Shadow was a genetically altered clone of Black Doom himself, and on top of that, the alien used him only so that he could take over the planet. He still couldn't believe his luck when Professor Gerald Robotnik's last message broke through and told him the true purpose of the Eclipse Cannon, a weapon that could destroy half the world and had left a massive hole in the moon several months ago. It was made just for the purpose of destroying the spaceship that Black Doom was on and ending the threat of the Black Arms. Shadow had harnessed the power of the Chaos Emeralds and faced his father, who had transformed into the monstrous Devil Doom. Shadow killed his father, and brought the Black Comet back into space, where Team Chaotix used the power of the Eclipse Cannon to destroy it, ending the threat of the Black Arms once and for all.

While the world was rebuilding following the invasion, Shadow had taken his leave of Westopolis and had set out to find his own place within it. Two weeks in, Shadow had entered a whole new territory far from Westopolis or Sonic and his pals. As the hedgehog rode on, he began to hear something... the grinding and clunking of a GUN Battle Mech.

Shadow frowned as he approached what was unmistakably a GUN roadblock, swarming with mechs, Beetle Drones, and normal foot soldiers. He slowed the bike to a stop, and a female GUN soldier with blonde hair approached him.

"Shadow the Hedgehog?" the soldier, who Shadow now recognized as Topaz, asked.

"Yes?" said Shadow, his voice as cool as ice.

"Commander Towers wants a word with you. We need you to come to headquarters," explained Topaz.

Shadow smirked. He'd been wondering when Towers would come after him. In fact, Shadow was surprised that he'd managed to get by this long, considering the fact that he'd single-handedly stopped an alien invasion when a whole peacekeeping force, the world's greatest heroes, and the single largest and most frequent threat to the world had been trampled.

"I'd been wondering when Towers would send someone after me… I might as well get this over with, then," said Shadow.

Topaz and some of the other soldiers blinked a few times in surprise. They'd all been expecting Shadow to be a bit more resistant to coming with them.

"W-well, then what are we standing around here for?" asked Topaz, leading Shadow to a waiting helicopter.

 _A Short While Later..._

Shadow and his escort were in the Command Center of GUN HQ, where various monitors displayed the reconstruction status of the six cities that the Black Arms had struck. Shadow cast a glance at the monitors, particularly the one showing what he recognized as Westopolis, the epicenter of the Black Arms invasion.

Shadow, Topaz, and their escort stopped at a particular door labeled "Commander A. Towers." Topaz dismissed the escort with a wave of her hand. They saluted, and marched away.

Topaz knocked on the door a couple times. "Come in," said a gruff male voice.

Topaz opened the door. Inside was a middle-aged man with storm-grey hair and heterochromic eyes, sitting at his desk pouring himself a glass of of whiskey. This was Towers, the Commander and leader of the Guardian Units of Nations.

"Sir, I've brought Shadow to you, as ordered, sir," said Topaz.

"Thank you, Topaz. You may go now," said Towers .

"Yes, sir," said Topaz. She snapped a salute, turned on her heel, and left, leaving Shadow alone with the Commander.

"Sit," said Towers, pointing to one of the nearby leather chairs. Shadow walked over to one of the and sat down, gazing intently at Commander Towers, who took a sip of whiskey before he spoke. "I suppose you're wondering why I've had you brought here."

Shadow crossed his arms. "More or less."

"You see, Shadow, after the Black Arms were destroyed, it quickly became obvious to the people of the United Federation and the whole world of Mobius, that not only are we not alone in this universe, but we are laughably out-gunned," explained Towers.

"And that means… what to me?" asked Shadow, who almost sounded bored with this conversation.

"I'll get to that part in a moment. I've been talking to The President, as well several other world leaders, and we've all come to the same conclusion: we either need to step up our Advanced Weapons Programs, or assemble a response team who can fight the battles that we cannot, or both," Towers continued. "We've already begun creating better weapons, but we're still in need of a response team with the skills and courage to use them."

Shadow chuckled and closed his eyes as he leaned his head back. "So, that's why you've brought me here… you want me to be a part of this response team of yours," he said.

"No, Shadow… I want you to _lead_ it."

Shadow chuckled and closed his eyes, a smirk evident on his face. Of course Towers would want him to lead a "response team." It was just like humans to try to ally themselves with anything more powerful than they were, provided it suited their needs. But, even so, Shadow was nonetheless interested.

"What if I say… no?" asked Shadow.

"Then, we'll persuade you," said a female voice from behind Shadow.

Shadow opened his eyes and turned around to see two new individuals standing behind him. One was a female and rather attractive bat with tan skin and white hair wearing a black bodysuit with a pink heart-shaped breastplate, white gloves, and black boots with pink steel toes. The second figure was a large red-and-black robot that looked as though it could handle anything that lived.

" _This unit does not believe persuasion will be required, Rouge,"_ said the robot in a deep, smooth voice. Shadow recognized the machine as E-123 Omega, a walking arsenal and the first and so far only Eggman robot ever to defy his creator that didn't get reduced to scrap metal, nor try to take over the world himself.

Shadow chuckled at the sight of them. Such was the mysterious power that Rouge had over him. Getting him to do whatever she wanted instead of what _he_ wanted. Sometimes Shadow wondered if he was in love with her, thus explaining the mysterious influence she had over the Ultimate Life Form.

"So, Shadow, final offer: are you in or out?" asked Towers.

Shadow thought about this for a moment. If he was a GUN agent, he could carry out his promise to Maria, and give the people of Mobius a chance to be happy...

 _Hold it, Shadow… it was GUN that killed Maria fifty years ago, remember? Wouldn't it be betraying her memory if you joined them?_ a voice in Shadow's head asked.

Shadow considered this for a moment… it had been a GUN soldier who had shot Maria… but, that had been fifty years ago, and Shadow had decided to put his past, save for his final promise to Maria, behind him forever. He knew who he was: Shadow the Goddamn Hedgehog, the Ultimate Life Form.

"Well, Shadow? We haven't got all day," said Towers.

Shadow looked the Commander dead in the eye and uttered two words that would set his future in motion.

"I'm in."

 _ **And thus concludes the opening chapter! If you liked what you saw here, be sure to fav, follow, and review, and I'll see you guys next time for Chapter One, where we get to meet some of the main villains of the story!**_


	2. Chapter I: The Doppelganger

_**Greetings, prospective readers! Welcome to the next chapter of Team Dark: Agents of GUN! Well, not really much else to talk about, so let's get this party started!**_

 _Chapter I: The Doppelganger_

 _Five years have passed since Shadow joined GUN. During those five years, Team Dark proved to be one of the best teams of agents the peacekeeping organization ever had in their employ. From foiling Dr. Eggman's more discrete plots to preventing doomsday in Soleanna, Team Dark quickly developed a reputation for being a virtually unstoppable band of agents._

 _As they established an unshakable reputation as an unstoppable war machine, they shot through the ranks of GUN like rockets. Only a year ago, Shadow had become a Captain, while Rouge and Omega had become Lieutenants, and had more decorations than a Christmas tree, not to mention over 150 combat missions under their belts._

 _All the while, Shadow and Rouge had become very close. They both knew that other agents and soldiers were whispering behind their backs that they had a crush on each other. Both of them frequently denied it, but still, the whispers continued. In reality, both Shadow and Rouge DID feel something for each other, but both were afraid to admit it to the other. For Shadow, it was because people he got close to personally had the tendency to die around him. For Rouge, it was the fear of rejection. So, to all appearances, their relationship remained strictly professional._

 _Even though Shadow had been told everything that GUN. knew about Project: Shadow, that still didn't keep the Black Blur from wondering one thing: what happened to the other prototypes of the Ultimate Life Form?_

 _Now, that question was about to be answered in a very, very, brutal fashion..._

 _Metropolis-HexCorp Energy Research Facility_

In a large laboratory, a team of scientists were studying and experimenting with a red liquid known as Lazerite, a very rare and dangerous substance that was currently being traded at incredibly high prices as fuel for energy reactors for things such as battleships. In fact, both G.U.N. and a " Kintobor," used this substance to fuel their fleets... although, the bean counters at the corporate office had a strong suspicion that "Kintobor" was a fake name used by a certain mad scientist bent on world domination... but, since he paid well and had an army of robots behind him, they couldn't really complain. This however did not stop a group of black clad soldiers from setting up several charges around a wall and set the timers to go.

"For the glory of Enerjak!" one of them yelled before activating the bombs.

Moments later, the bombs went off, throwing several scientists off their feet, before the soldiers stormed into the facility, taking everyone they could find hostage... but, not before someone managed to set off a distress signal. The scientist closest to the alarm was then knocked unconscious by the closest echidna, and pulled to the other hogtied scientists. "Ten, HUT!" the commander yelled the command, and the echidnas lined up at the hole in the wall. There, three shadowy figures stood. As the trio emerged into the light, it could be seen that one of them greatly resembled G.U.N. Agent Rouge, if she were a male, was smoking a cigarette and wore a sleek black tuxedo with a white shirt, both of which had holes to allow him to use his wings, and a black bowtie. He also wore black leather gloves, and black dress shoes. In other words, he looked like an old-fashioned gangster.

The robot looked almost exactly like Omega, except he had green eyes, and the parts of him that were black were white, and he had a white "E-102" symbol on his chest. The scientists also momentarily saw a large machine gun for the robot's right arm, before it folded up into a regular arm.

However, it was the third member of the group who sent chills up the scientists' spines. She looked almost exactly the same as Shadow the Hedgehog, except where he had black fur, crimson highlights, crimson eyes, and a powerful build, this hedgehog had a slender, sexier build, a black fur with magenta highlights, and piercing green eyes. She wore a black leather overcoat with a skintight suit of black leather body armor underneath, black gloves, purple, black, and white hover shoes, and a belt that had a variety of guns and knives on it.

"Well done. The Master will reward you for your actions," the femme fatale said. Stalking towards the scientists, she asked, "Now, then, perhaps you fine gentlemen will give me what I want now? More specifically, the Lazranite."

The scientist closest to her spat and said, "Eat dirt, bitch! You'll never have the Lazranite!"

The hedgehog turned to face the scientist. "Is that so? I rather beg to differ. As a matter of fact, _you're_ going to have the honor of telling me the codes I need to get into the Lazranite storage units... won't you?" she said, smirking down at the unruly scientist.

"Go to Hell," the scientist told the hedhgehog.

The femme fatale frowned, before she turned to the bat. "Rogue, can I have a smoke?" she asked.

Rogue smirked, knowing exactly what the she-devil had in mind. "Be my guest, Raven," the bat told the she-devil, handing her a cigarette and a lighter.

Raven lit up the cigarette, took a few puffs on it, and bent down in front of the scientist. "Now, then," she said, aiming the burning end of the cigarette in front of the scientist's eye. "The codes."

"Screw. You." The scientist retorted before spitting into Raven's eye. She lazily wiped it away, and soon grew a smile that would make Scourge, the "Reverse-Sonic" happy.

"I tried to warn you." Raven said as she dug the cigarette into the scientist's eye, twisting it in further as blood began to pour from the ruined eye. "Now, the codes."

 _Meanwhile, In The Skies Above HexCorp..._

Several GUN Dropships were flying high over the city streets. Their intelligence had reported that the invaders were part of an increasingly-active echidna faction known as the Dark Legion. On one of the dropships was Team Dark. Shadow, now clad in a black leather overcoat, black pants, black leather gloves, and a belt that held two handguns, an assault rifle, a sword in its scabbard, and a few knives, looked out from the open hatch, holding onto a hand railing.

Rouge, meanwhile, hadn't really changed all that much. Strapped to her waist was a small handgun, used whenever the odds called for it. As for E-123 Omega, he was the same as he'd always been.

"How much longer, Omega?" asked Shadow.

 _"Approximately 3.26 seconds until arrival, Captain,"_ said Omega. _"I recommend preparing for the drop!"_

"I don't get it. Why would echidnas, of all things, attack an energy research facility? I mean, what's the point?" asked Rouge. "And more importantly, I thought Knucklehead was the last of his kind."

"Evidently not. And besides, what is there to get?" asked Shadow, not even looking at Rouge. "We have our orders: drive the attackers out, and make sure they don't get their hands on anything."

 _"We're directly above the facility. Prepare for infiltration!"_ said Omega.

Shadow nodded and went to his motorcycle. He started up the engine as the dropship lowered for the drop. A ramp opened in the bottom of ship, and Shadow rode his motorcycle down it, with Rouge and Omega right behind him as he blasted his way into the energy facility.

"We got trouble! Get them!" yelled one of the invading foot soldiers before he and several others opened fire on Team Dark.

Shadow smirked as he leapt off his motorcycle and pulled out his assault rifle. Cocking it, he sprayed bullets onto some of the attacking echidnas, all of whom dropped like sacks of potatoes before Shadow's feet even hit the floor.

Rouge and Omega, meanwhile, dealt with the remaining echidnas, one of whom called for backup, only to be silenced a split-second later.

"Move out!" ordered Shadow.

Shadow, Rouge, Omega, and a small group of soldiers made their way into the interior of the facility, mowing down almost as many enemy troops as they lost. As they fought their way into the faciliy, Shadow and Rouge couldn't help but take notice of how well trained these echidna troopers were.

As Team Dark and their remaing troops pressed deeper into the facility, they reached a fork in the road, with three possible routes.

"All right, Rouge, you take the rest of the troops and head into that door," said Shadow, indicating the door on the far left. "Omega, you take the door on the right, I'll take the door on the center. Stay in touch via radio contact."

"Be careful," said Rouge as the three members of Team Dark went their seperate ways.

As Shadow entered the doorway and emerged into the room on the other side, he found that the place was quiet, very eerily so. Cocking his assault rifle, Shadow moved into the room slowly and cautiously.

The next thing Shadow knew, he'd been bowled over by something very fast, knocking the assault rifle out of his hands and sending it sliding across the floor. As soon as his vision cleared, Shadow's mind was thrown for a loop as he looked up at… himself. Or rather, what he'd probably look like if he were a female hedgehog rather than a male one. The doppelganger on top of Shadow had a sleeker, sexier build as opposed to his more strong and powerful one, had magenta highlights where he had crimson ones, and had piercing green eyes where he had burning crimson eyes.

"Rogue!" the mirror image said into a comlink in a female voice, "Take the prisoners to the base, will ya?"

" _Sure thing,"_ Shadow heard a male voice answer, " _but why?"_

"I'll be there in a sec. There's a problem that just came up that I need to deal with first." Turning back to Shadow, the copy got off of him, pulled out a pistol, and said, "Now, then, just who the Hell are you, and what gives you the right to jack my style?"

Shadow jumped up, pulled out his own pistol, and cocked his head to the side in confusion as he and his female doppelganger paced around each other. "I could very well ask you the same thing... but I think I've already got you pegged," he growled.

The genderbent Shadow clone laughed. "Is that so? Perhaps you could fill me in?" she asked.

"You're one of those Shadow Androids Dr. Eggman built, just with a different build, paint job and voice chip."

The doppelganger laughed. "Excuse me, 'Shadow Android?' Hate to break it to you, but I'm no robot," she snarled.

"Doesn't matter. I have my orders, and that includes taking you down," said Shadow.

With that, Shadow tried to fire his gun, but a blue Chaos Spear struck him in the chest, sending him sprawling to the ground.

The female Shadow stood there, her right palm outstretched, and sneered. "What is this bullshit?! First, you call me an android, and now you're trying to kill me?!" the copy said, kicking Shadow in the face as hard as she could. "From where I'm sitting, _you're_ the android. And you actually think you can just _kill_ me?! You can't kill me! _No one_ can kill me! I am the Ultimate Life Form created by Professor Gerald Robotnik. I saw him being taken prisoner aboard the Space Colony ARK fifty-five years ago from my containment tube. I heard that his granddaughter had died of a gunshot wound to the heart after the Guardian Units of Nations shut down Project: Shadow!"

A crazed gleam in her eyes, the female clone walked up to Shadow, and put a foot on his chest and her gun to his head to keep him down. "The ARK was empty for five years! _FIVE YEARS!_ " the duplicate snarled as she removed her foot and kicked Shadow in the face several times on her last two words.

"Do you have any idea how lonely I was?! No orders to take or give, no one to talk to! I had no purpose! It was enough to drive me crazy. In the end, I launched my own pod down to Mobius to start over. Now I have a great job, loyal friends, and plenty to live for!" the copy said, kicking Shadow in the face again. Before leaving, she said, "Chew on that while contemplating what Dr. Finitevus has in store for Mobius. Enerjak will rise again! And all shall kneel before him!"

With that, the female Shadow raced off leaving behind a cloud of dust as Shadow, his nose broken, pulled himself up off the ground and took off after his female doppelganger, who kept throwing blue Chaos Spears into his path to try to get him to trip and fall, but it was apparently to no avail, and it wasn't long before Shadow caught up to his female copy and tackled her to the ground on a landing platform outside the building.

"Ragh! You really don't know when to give up, do you, poser?! Very well, then, if you insist!" the female Shadow snarled as she pulled herself up off the ground before charging at Shadow and engaging him in hand-to-hand combat.

Backwards and forwards the two hedgehog dueled, neither of them giving an inch of ground, neither of them willing to try a Homing Attack or a Spin Dash to break through the other's defenses and risk taking an accidental one-step detour to the facility's lobby.

 _This girl… who is she? It's almost like I'm not fighting an android at all, but an actual female version of myself!_ thought Shadow as he and his female copy grappled one another, blood pouring from their noses and cut lips like a river. Unbeknownst to Shadow, his female doppelganger was having the exact same thoughts about him.

 _Gotta give this copyhog credit, I've never met anyone who can hold their own against the Ultimate Life Form. No doubt because he's one of those GUN robots, and yet… why can't I shake this feeling that he's more than just an android… why does it feel like this guy is… family?_ thought the female Shadow before the noise of an airship caught her attention.

"Some other time, poser!" said the female Shadow before giving Shadow a headbutt, dizzying him enough to give her time to pull out a pistol as an airship bearing an unknown insignia appeared behind her. Peering out the open hatch were the hedgehog's accomplices, Rogue and E-102 Gamma. But, even though she had Shadow in the perfect position to end him with a bullet to the face, that familial bond she'd started to feel stopped her from pulling the trigger.

"Raven! Either shoot him or get your ass over here! We gotta go!" called Rogue over the noise of the airship.

" _Our objective has been completed, we need to exfiltrate this location immediately!"_ called Gamma.

After another moment of hesitation, Raven lowered her gun and activated her Hover Shoes, taking off towards the airship with Shadow right behind her. The second Raven jumped into the airship, the vehicle took off into the distance, leaving Shadow behind, glaring in the direction the airship went.

 _ **And thus concludes Chapter One! Sorry for the long wait, guys I had a ton of other stuff and several other projects that needed attending to as well. But, anyways, if you liked what you saw here, then be sure to fave, follow, and review, and I'll see you guys next time!**_


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